#21 parameterise herg QC test

CardiacModelling · Aug 8, 2024 · b9ebc16 · b9ebc16
1 parent 264c697
commit b9ebc16
Showing 1 changed file with 43 additions and 50 deletions.
diff --git a/tests/test_herg_qc.py b/tests/test_herg_qc.py
@@ -8,8 +8,11 @@
 
 from pcpostprocess.hergQC import hERGQC
 
+WELLS = ['A01', 'A02', 'A03', 'A04', 'A05', 'D01']
+
 
 class TestHergQC(unittest.TestCase):
+
     def setUp(self):
         filepath = os.path.join('tests', 'test_data', '13112023_MW2_FF',
                                 'staircaseramp (2)_2kHz_15.01.07')
@@ -32,68 +35,58 @@ def setUp(self):
         self.test_trace_after = Trace(filepath2, json_file2)
 
     def test_run_qc(self):
-        tr_before = self.test_trace_before
-        tr_after = self.test_trace_after
-
-        v = tr_before.get_voltage()
-
-        times = tr_after.get_times()
-
-        self.assertTrue(np.all(np.isfinite(v)))
-        self.assertTrue(np.all(np.isfinite(times)))
+        for well in WELLS:
+            with self.subTest(well):
+                tr_before = self.test_trace_before
+                tr_after = self.test_trace_after
 
-        # Calculate sampling rate in (use kHz)
-        sampling_rate = int(1.0 / (times[1] - times[0]))
+                v = tr_before.get_voltage()
 
-        plot_dir = os.path.join(self.output_dir,
-                                'test_run_qc')
+                times = tr_after.get_times()
 
-        if not os.path.exists(plot_dir):
-            os.makedirs(plot_dir)
+                self.assertTrue(np.all(np.isfinite(v)))
+                self.assertTrue(np.all(np.isfinite(times)))
 
-        hergqc = hERGQC(sampling_rate=sampling_rate,
-                        plot_dir=plot_dir,
-                        voltage=v)
+                # Calculate sampling rate in (use kHz)
+                sampling_rate = int(1.0 / (times[1] - times[0]))
 
-        sweeps = [0, 1]
-        before = tr_before.get_trace_sweeps(sweeps)
-        after = tr_after.get_trace_sweeps(sweeps)
-        qc_vals_before = tr_before.get_onboard_QC_values(sweeps=sweeps)
-        qc_vals_after = tr_after.get_onboard_QC_values(sweeps=sweeps)
+                plot_dir = os.path.join(self.output_dir,
+                                        'test_run_qc')
 
-        res = {}
+                if not os.path.exists(plot_dir):
+                    os.makedirs(plot_dir)
 
-        # Spot check a few wells
-        # We could check all of the wells but it's time consuming
+                hergqc = hERGQC(sampling_rate=sampling_rate,
+                                plot_dir=plot_dir,
+                                voltage=v)
 
-        test_wells = ['A01', 'A02', 'A03', 'A04', 'A05', 'D01']
+                sweeps = [0, 1]
+                before = tr_before.get_trace_sweeps(sweeps)
+                after = tr_after.get_trace_sweeps(sweeps)
+                qc_vals_before = tr_before.get_onboard_QC_values(sweeps=sweeps)
+                qc_vals_after = tr_after.get_onboard_QC_values(sweeps=sweeps)
 
-        voltage_protocol = tr_before.get_voltage_protocol()
+                # Spot check a few wells
+                # We could check all of the wells but it's time consuming
 
-        for well in test_wells:
-            # Take values from the first sweep only
-            qc_vals_before_well = np.array(qc_vals_before[well])[0, :]
-            qc_vals_after_well = np.array(qc_vals_after[well])[0, :]
+                voltage_protocol = tr_before.get_voltage_protocol()
 
-            before_well = np.array(before[well])
-            after_well = np.array(after[well])
+                # Take values from the first sweep only
+                qc_vals_before_well = np.array(qc_vals_before[well])[0, :]
+                qc_vals_after_well = np.array(qc_vals_after[well])[0, :]
 
-            #  Assume that there are no discontinuities at the start or end of ramps
-            voltage_steps = [tstart
-                             for tstart, tend, vstart, vend in
-                             voltage_protocol.get_all_sections() if vend == vstart]
+                before_well = np.array(before[well])
+                after_well = np.array(after[well])
 
-            passed, qcs = hergqc.run_qc(voltage_steps,
-                                        times, before_well, after_well,
-                                        qc_vals_before_well,
-                                        qc_vals_after_well, n_sweeps=2)
+                #  Assume that there are no discontinuities at the start or end of ramps
+                voltage_steps = [tstart
+                                 for tstart, tend, vstart, vend in
+                                 voltage_protocol.get_all_sections() if vend == vstart]
 
-            logging.debug(well, passed)
-            res[well] = passed
+                passed, qcs = hergqc.run_qc(voltage_steps,
+                                            times, before_well, after_well,
+                                            qc_vals_before_well,
+                                            qc_vals_after_well, n_sweeps=2)
 
-        self.assertTrue(res['A01'])
-        self.assertTrue(res['A02'])
-        self.assertTrue(res['A03'])
-        self.assertTrue(res['A04'])
-        self.assertFalse(res['A05'])
-        self.assertFalse(res['D01'])
+                logging.debug(well, passed)
+                self.assertTrue(passed)